Women’s empowerment is considered to play a crucial role in food and nutrition security. We aimed to explore the relationship between women’s empowerment and food and nutrition security, in rural Pakistan. Methods: To estimate women’s empowerment, we developed a Rural Women Composite Empowerment Index incorporating nine domains. For indicators of food and nutritional data we used data of 1879 rural households from Pakistan Rural Household Panel Survey (PRHPS). Food insecurity was measured through a caloric intake approach; nutrition insecurity was measured through recommended nutrient intake (RNI). Using the Rural Women’s Composite Empowerment Index (RWCEI), we employed multi-level mixed-effect regression analysis. Results: The domains of traveling safely (21%), time allocated to tasks (20%), and (lack of) domestic violence (19%) were the most significant domains in defining empowerment of rural woman. The prevalence of food and nutrition insecurity were 33% and 50% respectively. Regression analysis found a positive and significant relationship between women’s empowerment and food and nutrition security–the proportion of household who were food and nutritionally secure in empowered households was 70% and 98% respectively. Conclusions: Developing programmes and policies to improve the range of domains of women’s empowerment requires a focussed policy agenda, bringing together policy makers from a number of different sectors including education, economy, communications, technology and agriculture. Women’s empowerment has the potential to make positive changes not only in food and nutrition security, but in all aspects of family health and wellbeing.